Pseudophryne corroboree

corroboree frog

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank aPseCor3: GCA_028390025.1 aPseCor3: GCA_028390055.1
ENA aPseCor3: GCA_028390025.1 aPseCor3: GCA_028390055.1
UCSC Genome Browser aPseCor3: GCA_028390025.1 aPseCor3: GCA_028390055.1

metadata.yaml (view) (edit on github)
species:
  name: Pseudophryne corroboree
  individuals:
  - short_name: aPseCor3
  short_name: aPseCor
  taxon_id: 495146
  common_name: corroboree frog
  genome_size: 8557000000
  genome_size_method: GoAT
  order:
    name: Anura
  family:
    name: Myobatrachidae
  project: [ vgp ]
CC BY-SA 3.0 Andrew c (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aPseCor3 820.24 Gbp 95.86x 2.0 TiB
PacBio HiFi (.fq) aPseCor3 230.31 Gbp 26.91x 175.0 GiB
PacBio HiFi (.bam) aPseCor3 229.32 Gbp 26.80x 788.4 GiB
Bionano aPseCor3 N/A 1241.01x 17.4 GiB
Arima aPseCor3 381.02 Gbp 44.53x 188.4 GiB
Illumina aPseCor1 387.72 Gbp 45.31x 184.5 GiB
aPseCor2 366.86 Gbp 42.87x 174.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 8.56 Gbp.
Last upload on 14 March 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aPseCor1 Illumina 387.72 Gbp 45.31x 184.5 GiB
aPseCor2 Illumina 366.86 Gbp 42.87x 174.0 GiB
aPseCor3 PacBio HiFi (subreads) 820.24 Gbp 95.86x 2.0 TiB
PacBio HiFi (.fq) 230.31 Gbp 26.91x 175.0 GiB
PacBio HiFi (.bam) 229.32 Gbp 26.80x 788.4 GiB
Bionano N/A 1241.01x 17.4 GiB
Arima 381.02 Gbp 44.53x 188.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 8.56 Gbp.
Last upload on 14 March 2023.
Assemblies
Individual 3 Primary Assembly
No assembly available.


Contigs Scaffolds
NG LG Len LG Len
10 - - - -
20 - - - -
30 - - - -
40 - - - -
50 - - - -
60 - - - -
70 - - - -
80 - - - -
90 - - - -
100 - - - -
0.000x - 0.0 Mbp - 0.0 Mbp
Individual 3 Alternate Assembly
Version assembly_curated from 17 December 2022
aPseCor3.alt.cur.20221217.fasta.gz (158.3 KiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.000x 1 0.54 Mbp 1 0.54 Mbp
NG based on genome size 8.56 Gbp.
Individual 3 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 August 2022
aPseCor3.HiC.hap1.20220806.fasta.gz (2.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 31 22.87 Mbp 1 1.22 Gbp
20 77 15.59 Mbp 2 1.04 Gbp
30 141 11.71 Mbp 3 0.93 Gbp
40 224 9.09 Mbp 4 0.82 Gbp
50 330 7.19 Mbp 5 0.68 Gbp
60 467 5.40 Mbp 6 0.66 Gbp
70 655 3.87 Mbp 8 466.06 Mbp
80 927 2.52 Mbp 11 206.57 Mbp
90 1386 1.36 Mbp 16 76.73 Mbp
100 2557 361.00 Kbp 424 0.59 Mbp
1.043x 5957 8.93 Gbp 3526 8.95 Gbp
NG based on genome size 8.56 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 17 December 2022
aPseCor3.hap2.cur.20221217.fasta.gz (2.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 28 22.40 Mbp 0 1.25 Gbp
20 75 15.29 Mbp 1 1.06 Gbp
30 141 11.59 Mbp 2 0.95 Gbp
40 224 9.09 Mbp 3 0.85 Gbp
50 330 7.10 Mbp 4 0.85 Gbp
60 469 5.22 Mbp 5 0.81 Gbp
70 670 3.60 Mbp 6 0.52 Gbp
80 964 2.31 Mbp 8 483.89 Mbp
90 1474 1.18 Mbp 10 366.57 Mbp
100 2906 268.00 Kbp 408 412.31 Kbp
1.034x 5826 8.85 Gbp 3127 8.87 Gbp
NG based on genome size 8.56 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/aPseCor3_hap2.yaml (view)
species: Pseudophryne corroboree
specimen: aPseCor3
projects: 
  - vgp
hap1: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/assembly_vgp_HiC_2.0/aPseCor3.HiC.hap1.20220806.fasta.gz
hap2: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/assembly_vgp_HiC_2.0/aPseCor3.HiC.hap2.20220806.fasta.gz
pretext_hap1: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/aPseCor3_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/aPseCor3_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/assembly_vgp_HiC_2.0/evaluation/aPseCor3_png/
pacbio_read_dir: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Pseudophryne_corroboree/aPseCor3/genomic_data/bionano/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - solve (3.7.0+galaxy0)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: Please curate hap2 ( aPseCor3.HiC.hap2.20220806.fasta.gz ), as it looks like the more complete assembly between the two of them. I am including the hap1 paths here in case they would be useful. 
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.